As a method for detecting an interaction between a protein and a substance, a method wherein mRNA-protein assignment molecules prepared by linking mRNAs to the proteins encoded thereby via covalent bonds are used for obtaining the amino acid sequence information of the protein as base sequence information of DNA is known as the in vitro virus (IVV) method (Patent Documents 1 to 3). By using the IVV method and a Sanger-type DNA sequencer, proteome analysis has been carried out (Non-patent Document 2, Non-patent Document 3 and Non-patent Document 4). Since, in the conventional Sanger-based sequence analysis, sequence analysis was possible for data corresponding to only a part (about 1000 reads) of the library, it has been practically difficult to cover the whole library space (false-negative problem).
Attempts have been made to introduce a next-generation sequencer to transcriptome and proteome analyses to obtain a large amount of information on intermolecular interactions among proteins/DNAs/RNAs (Non-patent Document 4). However, it is known that false positives are contained in the obtained data, and that acquisition of a large amount of data results in acquisition of a large amount of false-positive data. Therefore, elimination of the false positives (improvement of reliability) has been demanded.